Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

Biomolecular pathways are built from diverse types of pairwise interactions, ranging from physical protein-protein interactions and modifications to indirect regulatory relationships. One goal of systems biology is to bridge three aspects of this complexity: the growing body of high-throughput data assaying these interactions; the specific interactions in which individual genes participate; and the genome-wide patterns of interactions in a system of interest. Here, we describe methodology for simultaneously predicting specific types of biomolecular interactions using high-throughput genomic data. This results in a comprehensive compendium of whole-genome networks for yeast, derived from ∼3,500 experimental conditions and describing 30 interaction types, which range from general (e.g. physical or regulatory) to specific (e.g. phosphorylation or transcriptional regulation). We used these networks to investigate molecular pathways in carbon metabolism and cellular transport, proposing a novel connection between glycogen breakdown and glucose utilization supported by recent publications. Additionally, 14 specific predicted interactions in DNA topological change and protein biosynthesis were experimentally validated. We analyzed the systems-level network features within all interactomes, verifying the presence of small-world properties and enrichment for recurring network motifs. This compendium of physical, synthetic, regulatory, and functional interaction networks has been made publicly available through an interactive web interface for investigators to utilize in future research at http://function.princeton.edu/bioweaver/

TRAPP stably associates with the Golgi and is required for vesicle docking

Bet3p, a component of a large novel complex called TRAPP, acts upstream of endoplasmic reticulum (ER)–Golgi SNAREs. Unlike the SNAREs, which reside on multiple compartments, Bet3p is localized exclusively to Golgi membranes. While other proteins recycle from the Golgi to the ER, Bet3p and other TRAPP subunits remain associated with this membrane under conditions that block anterograde traffic. We propose that the persistent localization of TRAPP to the Golgi may be important for its role in docking vesicles to this membrane. Consistent with this proposal, we find that transport vesicles fail to bind to Golgi membranes in vitro in the absence of Bet3p. Binding is restored by the addition of cytosol containing Bet3p. These findings indicate that TRAPP stably associates with the Golgi and is required for vesicle docking